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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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pre-process #127

Closed hermeseduardo closed 7 years ago

hermeseduardo commented 7 years ago

Hi, should we do quality trimming before using sga preqc, assembly with sga? In my case I have Illumina paired end data. Any chance to allow hybrid assembly (Illumina+PacBio) data in the future? thanks

jts commented 7 years ago

I suggest you don't quality trim before using preqc. After looking at the preqc report you can decide whether to trim or not. I typically do not suggest to trim unless the error rate at the ends of the reads is extremely high.

It is very unlikely that I will extend SGA to allow hybrid assembly, sorry.

hermeseduardo commented 7 years ago

OK thanks!!

2016-08-29 18:48 GMT+02:00 Jared Simpson notifications@github.com:

I suggest you don't quality trim before using preqc. After looking at the preqc report you can decide whether to trim or not (I typically do not suggest to trim unless the error rate at the ends of the reads is extremely high).

It is very unlikely that I will extend SGA to allow hybrid assembly, sorry.

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